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* dev-python/bedtools: move from sci-biology, version bump 0.10.0HEADmasterMichael Schubert7 days6-50/+5
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1285 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-bioloy/gffutils: version bump 0.13; fix testsMichael Schubert7 days4-47/+33
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/pyfaidx: version bump 0.8.1.1Michael Schubert7 days7-52/+27
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/bx-python: version bump 0.12.0, enable testsMichael Schubert9 days7-111/+51
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1287 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* profiles: mask sci-biology/BBmapAndrew Ammerlaan9 days1-2/+3
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/datrie: fix gcc14 compileMichael Schubert2024-07-111-1/+3
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1280 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/snakemake: version bump 8.16.0Michael Schubert2024-07-112-14/+14
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/snakemake-interface-storage-plugins: version bump 3.2.3Michael Schubert2024-07-112-1/+1
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/snakemake-interface-executor-plugins: version bump 9.2.0Michael Schubert2024-07-112-1/+1
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/rich-click: version bump 1.8.3Michael Schubert2024-07-112-3/+3
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1284 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/plac: version bump 1.4.3Michael Schubert2024-07-112-2/+2
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1283 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/dpath: version bump 2.2.0 and add test depsMichael Schubert2024-07-112-2/+9
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1282 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/multiqc: version bump 1.23Michael Schubert2024-07-112-1/+1
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1281 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/awkward: add 2.6.6Alexander Puck Neuwirth2024-06-272-0/+45
| | | | Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* dev-python/awkward-cpp: add 35Alexander Puck Neuwirth2024-06-272-0/+27
| | | | Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* dev-python/archspec: add 0.2.4, drop 0.2.2, drop 0.1.4Alexander Puck Neuwirth2024-06-273-22/+10
| | | | Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* dev-python/boost-histogram: add 1.4.1, drop 1.4.0Alexander Puck Neuwirth2024-06-272-1/+2
| | | | Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* sci-mathematics/Oid: Fix java, update URLsAlexander Puck Neuwirth2024-06-272-8/+29
| | | | | | Co-authored-by: Andrew Nowa Ammerlaan <andrewammerlaan@gentoo.org> Closes: https://github.com/gentoo/sci/pull/1240 Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* sci-physics/sherpa: new package, add 3.0.0_beta1, 9999Alexander Puck Neuwirth2024-06-274-0/+216
| | | | | Closes: https://github.com/gentoo/sci/pull/1279 Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* sci-physics/herwig: new package, add 7.3.0Alexander Puck Neuwirth2024-06-273-0/+92
| | | | | | Co-authored-by: Andrew Nowa Ammerlaan <andrewammerlaan@gentoo.org> Closes: https://github.com/gentoo/sci/pull/1271 Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* sci-physics/evtgen: new package, 02.02.01Alexander Puck Neuwirth2024-06-273-0/+63
| | | | | Co-authored-by: Andrew Nowa Ammerlaan <andrewammerlaan@gentoo.org> Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* sci-physics/photos: new package, add 3.64Alexander Puck Neuwirth2024-06-273-0/+106
| | | | | Co-authored-by: Andrew Nowa Ammerlaan <andrewammerlaan@gentoo.org> Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* sci-physics/tauola: update EAPI 7 -> 8Alexander Puck Neuwirth2024-06-273-2/+113
| | | | | Co-authored-by: Andrew Nowa Ammerlaan <andrewammerlaan@gentoo.org> Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* sci-physics/mcfm: Adjust oneloop versionAlexander Puck Neuwirth2024-06-271-1/+1
| | | | | Closes: https://github.com/gentoo/sci/pull/1267 Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* sci-physics/openloops: new package, add 2.1.2Alexander Puck Neuwirth2024-06-275-0/+177
| | | | Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* sci-physics/cuttools: new package, add 1.8.2Alexander Puck Neuwirth2024-06-274-0/+101
| | | | | Co-authored-by: Andrew Nowa Ammerlaan <andrewammerlaan@gentoo.org> Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* sci-physics/oneloop: add 3.6, drop 2020.07.31Alexander Puck Neuwirth2024-06-276-47/+228
| | | | Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* dev-python/sphinxcontrib-napoleon: enable py3.12Andrew Ammerlaan2024-06-191-1/+1
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/snakemake: version 7.32.4 is compat with py3.12Michael Schubert2024-06-192-9/+9
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1278 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-mathematics/pulp: tests pass with python3.12Michael Schubert2024-06-191-1/+1
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/snakemake: add version 8Michael Schubert2024-06-192-0/+75
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/smart-open: py3.12 compat; disable tests (broken in py3.11)Michael Schubert2024-06-191-5/+6
| | | | | | | upstream URL update is automatic forward Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/google-cloud-storage: version bump 2.17.0Michael Schubert2024-06-192-3/+4
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/datrie: py3.12 compatMichael Schubert2024-06-191-1/+1
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/snakemake-storage-plugins: add ebuildMichael Schubert2024-06-193-0/+41
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/snakemake-report-plugins: add ebuildMichael Schubert2024-06-193-0/+38
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/snakemake-executor-plugins: add ebuildMichael Schubert2024-06-193-0/+40
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/snakemake-interface-common: add ebuildMichael Schubert2024-06-193-0/+39
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/immutables: add ebuildMichael Schubert2024-06-193-0/+38
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/conda-inject: add ebuildMichael Schubert2024-06-193-0/+38
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/argparse-dataclass: add ebuildMichael Schubert2024-06-193-0/+36
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/throttler: py3.12 compatMichael Schubert2024-06-191-1/+1
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/stopit: py3.12 compatMichael Schubert2024-06-191-1/+1
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/reretry: py3.12 compatMichael Schubert2024-06-191-1/+1
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/connection_pool: py3.12 compatMichael Schubert2024-06-191-1/+1
| | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/multiqc: version bump 1.22.2Michael Schubert2024-06-194-45/+43
| | | | | | Signed-off-by: Michael Schubert <mschu.dev@gmail.com> Closes: https://github.com/gentoo/sci/pull/1277 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* */*: drop distutils_enable_tests --installAndrew Ammerlaan2024-06-173-3/+3
| | | | | | TODO: port these packages to pep517, and fix tests Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/imagej: ant-core deprecatedIsrael Hernandez2024-06-172-2/+0
| | | | | | | | | | | | | | Signed-off-by: IAHMCOL <IAHMCOL@thejabberwocky.net> This commit removes dev-java/ant-core from dependencies This has been deprecated, and it gets automatically used with ant2 Latest updates had depclean dev-java/ant-core, and the packages still builds after dependency removal see: https://packages.gentoo.org/packages/dev-java/ant-core Closes: https://github.com/gentoo/sci/pull/1275 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/vector: add 1.4.1, drop 1.4.0Alexander Puck Neuwirth2024-06-112-1/+1
| | | | Signed-off-by: Alexander Puck Neuwirth <alexander@neuwirth-informatik.de>
* sci-mathematics/pulp: Added pulp version 2.8.0 + python3.12Tomas Fabrizio Orsi2024-06-112-0/+22
| | | | | | Signed-off-by: Tomas Fabrizio Orsi <torsi@fi.uba.ar> Closes: https://github.com/gentoo/sci/pull/1273 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>